The empty body subplot covers Professor X's return. As for Phoenix, it should not be too difficult an exercise in screenwriting to cover, considering how multi-faceted the Phoenix force is in the comics.

There is no Phoenix Force in these films and at this point, with Shaw dead,the Hellfire club probably never coming back and doubting very much the Shiar are ever introduced, there is no reason to bring the phoenix force into the films. While I don't see the franchise rebooting any time soon, there is no doubt that X-men: The Lat Stand and X-men Origins: Wolverine did damage to the franchise. I'm sure some people would like to blame a new cast on First Class under preforming, but I'm sure that many people didn't want to get duped a third time. Also the original cast returning doesn't guarantee success, trailers and marketing will have to be good to ensure DOFP is profitable. The marketing for the Wolverine doesn't make me particularly hopeful.